Mercurial > repos > ethevenot > qualitymetrics

comparison qualitymetrics_script.R @ 1:6d3b7b6573d8 draft

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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 60328240b89497f9dc7633b10b2a550b10da00c7
author ethevenot
date Fri, 21 Oct 2016 12:56:22 -0400
parents b4f5b5bc01dd
children 596320b84315
comparison
equal deleted inserted replaced
0:b4f5b5bc01dd 1:6d3b7b6573d8
422 text(1, 0.65, adj=0, cex = 1.1, labels = paste0("min: ", signif(min(datMN, na.rm=TRUE), 2))) 422 text(1, 0.65, adj=0, cex = 1.1, labels = paste0("min: ", signif(min(datMN, na.rm=TRUE), 2)))
423 text(1, 0.55, adj=0, cex = 1.1, labels = paste0("median: ", signif(median(datMN, na.rm=TRUE), 2))) 423 text(1, 0.55, adj=0, cex = 1.1, labels = paste0("median: ", signif(median(datMN, na.rm=TRUE), 2)))
424 text(1, 0.45, adj=0, cex = 1.1, labels = paste0("mean: ", signif(mean(datMN, na.rm=TRUE), 2))) 424 text(1, 0.45, adj=0, cex = 1.1, labels = paste0("mean: ", signif(mean(datMN, na.rm=TRUE), 2)))
425 text(1, 0.35, adj=0, cex = 1.1, labels = paste0("max: ", signif(max(datMN, na.rm=TRUE), 2))) 425 text(1, 0.35, adj=0, cex = 1.1, labels = paste0("max: ", signif(max(datMN, na.rm=TRUE), 2)))
426 if("sampleType" %in% colnames(samDF) && 426 if("sampleType" %in% colnames(samDF) &&
427 "pool" %in% samDF[, "sampleType"]) 427 "pool" %in% samDF[, "sampleType"]) {
428 poolCvNanVl <- is.nan(varDF[, "pool_CV"])
428 text(1, 429 text(1,
429 0.25, 430 0.25,
430 adj=0, cex = 1.1, 431 adj=0, cex = 1.1,
431 labels = paste0("pool CV < ", 432 labels = paste0("pool CV < ",
432 round(thrVn["poolCv"] * 100), "%: ", 433 round(thrVn["poolCv"] * 100), "%: ",
433 round(sum(varDF[, "pool_CV"] < thrVn["poolCv"]) / nrow(varDF) * 100), 434 round(sum(varDF[!poolCvNanVl, "pool_CV", drop = FALSE] < thrVn["poolCv"]) / nrow(varDF) * 100),
434 "%")) 435 "%"))
436 }
435 437
436 text(1, 0.1, adj=0, labels = paste0("Thresholds used in plots:")) 438 text(1, 0.1, adj=0, labels = paste0("Thresholds used in plots:"))
437 text(1, 0, adj=0, labels = paste0(" p-value = ", thrVn["pvalue"])) 439 text(1, 0, adj=0, labels = paste0(" p-value = ", thrVn["pvalue"]))
438 440
439 ## dri: Analytical drift 441 ## dri: Analytical drift